Ribosomal RNA genes have long been a favoured locus in phylogenetic and metabarcoding studies. Within a genome, rRNA loci are organized as tandem repeated arrays and the copies are homogenized through the process of concerted evolution. However, some level of rRNA variation (intragenomic polymorphism) is known to persist and be maintained in the genomes of many species. In nematode worms, the extent of rRNA polymorphism (RP) across species and the evolutionary and life history factors that contribute to the maintenance of intragenomic RP is largely unknown. Here, we present an extensive analysis across 30 terrestrial nematode species representing a range of free-living and parasitic taxa isolated worldwide. Our results indicate that RP is common and widespread, ribosome function appears to be maintained despite mutational changes, and intragenomic variants are stable in the genome and neutrally evolving. However, levels of variation were varied widely across rRNA locus and species, with some taxa observed to lack RP entirely. Higher levels of RP were significantly correlated with shorter generation time and high reproductive rates, and population-level factors may play a role in the geographic and phylogenetic structuring of rRNA variants observed in genera such as Rotylenchulus and Pratylenchus. Although RP did not dramatically impact the clustering and recovery of taxa in mock metabarcoding analyses, the present study has significant implications for global biodiversity estimates of nematode species derived from environmental rRNA amplicon studies, as well as our understanding of the evolutionary and ecological factors shaping genetic diversity across the nematode Tree of Life.

中文翻译：

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线虫内基因组rRNA多态性的普遍流行但形成鲜明对比的模式：对系统发育，物种界定和生活史推断的影响。

核糖体RNA基因长期以来一直是系统发育和元条形码研究中的首选位点。在基因组内，rRNA基因座被组织为串联重复阵列，并且拷贝通过协调进化的过程被均质化。但是，已知一定水平的rRNA变异（整合基因组多态性）会持续存在并保持在许多物种的基因组中。在线虫蠕虫中，跨物种的rRNA多态性（RP）的程度以及有助于维持基因组内RP的进化和生活史因素尚不清楚。在这里，我们对30种陆地线虫物种进行了广泛的分析，这些物种代表了世界范围内一系列自由活动和寄生类群。我们的结果表明，RP是常见且广泛存在的，尽管发生了突变，核糖体功能似乎仍然得以维持，基因组内变体在基因组中是稳定的，并且是中性进化的。但是，变异水平在rRNA基因座和物种之间差异很大，观察到一些分类群完全缺乏RP。较高的RP水平与较短的产生时间和较高的生殖率显着相关，种群水平的因素可能在诸如Rotylenchulus和Pratylenchus等属中观察到的rRNA变异的地理和系统发育结构中。尽管RP并未在模拟元条形码分析中显着影响分类群的聚类和恢复，但本研究对从环境rRNA扩增子研究得出的线虫物种的全球生物多样性估计具有重大意义，